chr7-55240511-A-G

Variant names:

• chr7-55240511-A-G
• rs76795398
• ENST00000626532.1:n.338-1845T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000626532.1(ELDR):​n.338-1845T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 152,242 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.027 (95 hom., cov: 32)
• Consequence: ELDR ENST00000626532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 1 publications found

Genes affected

ELDR (HGNC:49511): (EGFR long non-coding downstream RNA) Predicted to act upstream of or within regulation of gene expression and response to wounding. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.027 (4114/152242) while in subpopulation NFE AF = 0.0424 (2883/68016). AF 95% confidence interval is 0.0411. There are 95 homozygotes in GnomAd4. There are 1941 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 95 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626532.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELDR	NR_110426.1		n.338-1845T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELDR	ENST00000626532.1	TSL:4	n.338-1845T>C		intron	N/A
	ELDR	ENST00000782315.1		n.347-1845T>C		intron	N/A
	ELDR	ENST00000782316.1		n.298-1845T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 4117 AN: 152124 Hom.: 95 Cov.: 32

Gnomad AFR AF: 0.00637

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0244

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0270 AC: 4114 AN: 152242 Hom.: 95 Cov.: 32 AF XY: 0.0261 AC XY: 1941 AN XY: 74428

African (AFR) AF: 0.00636 AC: 264 AN: 41540

American (AMR) AF: 0.0234 AC: 358 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0269 AC: 130 AN: 4824

European-Finnish (FIN) AF: 0.0179 AC: 190 AN: 10602

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0424 AC: 2883 AN: 68016

Other (OTH) AF: 0.0232 AC: 49 AN: 2112

Alfa AF: 0.0369 Hom.: 28

Bravo AF: 0.0264

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
DANN	Benign	0.46
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs76795398; hg19: chr7-55308204;